It is a stupid argument to say aircraft fly over war-zones all the time. They don't fly over war-zones where the belligerents have both the capability of bringing down a commercial aircraft at cruising altitude, and where they lack the technical competence or basic command control structure to guarantee safety to civilian aircraft. I've seen articles dated 29th June were the rebels already claimed to have captured and to have the capability of firing an SA-11. If so, the airspace should have been closed immediately, and failing that, the airline risk assessment should have re-routed aircraft.
For anyone who has flown into Kabul recently, they will know that the aircraft are stacked and perform approaches so as to minimize the chance of being attacked with a manpad (shoulder launched rocket). If the capability or intentions of belligerents change, all aircraft risk assessment should change immediately rather than wait for the next monthly update. That it was not seemingly done in this case amounts to negligence.